SPAAM-community / AncientMetagenomeDir

Repository containing lists of all published ancient metagenomic (and related) samples and libraries
http://www.spaam-community.org/AncientMetagenomeDir/
Creative Commons Attribution 4.0 International
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Guellil2022 #989

Closed DianaSpurite closed 2 years ago

DianaSpurite commented 2 years ago

Pull Request

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Publication Information

This pull request is to add samples from the following publication(s):

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Checklist

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Reference

This pull request is to correct samples from the following publication(s):

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Description

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Checklist

github-actions[bot] commented 2 years ago

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━┩ │ England │ 538 │ geo_loc_name │ 'England' is not │ │ │ │ │ an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ geo_loc_name.json │ │ England │ 537 │ geo_loc_name │ 'England' is not │ │ │ │ │ an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ geo_loc_name.json │ │ Haemophilus influenzae │ 537 │ singlegenome_spe… │ 'Haemophilus │ │ │ │ │ influenzae' is │ │ │ │ │ not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ singlegenome_spec │ │ │ │ │ ies.json │ │ teeth │ 538 │ material │ 'teeth' is not an │ │ │ │ │ accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ material.json │ │ teeth │ 537 │ material │ 'teeth' is not an │ │ │ │ │ accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ material.json │ └────────────────────────┴─────────────┴───────────────────┴───────────────────┘ The following type of errors were found: • DatasetValidationError ```
github-actions[bot] commented 2 years ago

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━┩ │ teeth │ 538 │ material │ 'teeth' is not an │ │ │ │ │ accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ material.json │ │ England │ 538 │ geo_loc_name │ 'England' is not │ │ │ │ │ an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ geo_loc_name.json │ │ teeth │ 537 │ material │ 'teeth' is not an │ │ │ │ │ accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ material.json │ │ England │ 537 │ geo_loc_name │ 'England' is not │ │ │ │ │ an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ geo_loc_name.json │ │ Haemophilus influenzae │ 537 │ singlegenome_spe… │ 'Haemophilus │ │ │ │ │ influenzae' is │ │ │ │ │ not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ singlegenome_spec │ │ │ │ │ ies.json │ └────────────────────────┴─────────────┴───────────────────┴───────────────────┘ The following type of errors were found: • DatasetValidationError ```
github-actions[bot] commented 2 years ago

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━┩ │ Haemophilus influenzae │ 537 │ singlegenome_spe… │ 'Haemophilus │ │ │ │ │ influenzae' is │ │ │ │ │ not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ singlegenome_spec │ │ │ │ │ ies.json │ └────────────────────────┴─────────────┴───────────────────┴───────────────────┘ The following type of errors were found: • DatasetValidationError ```
DianaSpurite commented 2 years ago

Here I need an approval for the added enum in order for the sample and library commit to pass the checks, as far as I understand.

github-actions[bot] commented 2 years ago

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━┩ │ Haemophilus influenzae │ 537 │ singlegenome_spe… │ 'Haemophilus │ │ │ │ │ influenzae' is │ │ │ │ │ not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-com │ │ │ │ │ munity.github.io/ │ │ │ │ │ AncientMetagenome │ │ │ │ │ Dir/assets/enums/ │ │ │ │ │ singlegenome_spec │ │ │ │ │ ies.json │ └────────────────────────┴─────────────┴───────────────────┴───────────────────┘ The following type of errors were found: • DatasetValidationError ```
github-actions[bot] commented 2 years ago

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json All is good, no errors were found !

Ancient Metagenome Host Associated Libraries

Checking ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries.tsv against schema ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Libraries

Checking ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries.tsv against schema ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries_schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━┩ │ doi.org/10.1186/s13059-021-02580-z │ 2101 │ data_publi… │ 'doi.org/10 │ │ │ │ │ .1186/s1305 │ │ │ │ │ 9-021-02580 │ │ │ │ │ -z' does │ │ │ │ │ not match │ │ │ │ │ '^10.\\d{4, │ │ │ │ │ 9}\\/[^,]+$ │ │ │ │ │ ' │ │ doi.org/10.1186/s13059-021-02580-z │ 2104 │ data_publi… │ 'doi.org/10 │ │ │ │ │ .1186/s1305 │ │ │ │ │ 9-021-02580 │ │ │ │ │ -z' does │ │ │ │ │ not match │ │ │ │ │ '^10.\\d{4, │ │ │ │ │ 9}\\/[^,]+$ │ │ │ │ │ ' │ │ doi.org/10.1186/s13059-021-02580-z │ 2103 │ data_publi… │ 'doi.org/10 │ │ │ │ │ .1186/s1305 │ │ │ │ │ 9-021-02580 │ │ │ │ │ -z' does │ │ │ │ │ not match │ │ │ │ │ '^10.\\d{4, │ │ │ │ │ 9}\\/[^,]+$ │ │ │ │ │ ' │ │ doi.org/10.1186/s13059-021-02580-z │ 2102 │ data_publi… │ 'doi.org/10 │ │ │ │ │ .1186/s1305 │ │ │ │ │ 9-021-02580 │ │ │ │ │ -z' does │ │ │ │ │ not match │ │ │ │ │ '^10.\\d{4, │ │ │ │ │ 9}\\/[^,]+$ │ │ │ │ │ ' │ └────────────────────────────────────┴─────────────┴─────────────┴─────────────┘ The following type of errors were found: • DatasetValidationError ```
github-actions[bot] commented 2 years ago

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json All is good, no errors were found !

Ancient Metagenome Host Associated Libraries

Checking ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries.tsv against schema ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Libraries

Checking ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries.tsv against schema ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Libraries

Checking ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies.tsv against schema ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies_schema.json All is good, no errors were found !

github-actions[bot] commented 2 years ago

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json All is good, no errors were found !

Ancient Metagenome Host Associated Libraries

Checking ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries.tsv against schema ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Libraries

Checking ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries.tsv against schema ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Libraries

Checking ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies.tsv against schema ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies_schema.json All is good, no errors were found !

github-actions[bot] commented 2 years ago

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json All is good, no errors were found !

Ancient Metagenome Host Associated Libraries

Checking ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries.tsv against schema ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Libraries

Checking ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries.tsv against schema ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Libraries

Checking ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies.tsv against schema ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies_schema.json All is good, no errors were found !

github-actions[bot] commented 2 years ago

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json All is good, no errors were found !

Ancient Metagenome Host Associated Libraries

Checking ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries.tsv against schema ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Libraries

Checking ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries.tsv against schema ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Libraries

Checking ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies.tsv against schema ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies_schema.json All is good, no errors were found !

github-actions[bot] commented 2 years ago

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json All is good, no errors were found !

Ancient Metagenome Host Associated Libraries

Checking ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries.tsv against schema ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Libraries

Checking ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries.tsv against schema ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Libraries

Checking ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies.tsv against schema ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies_schema.json All is good, no errors were found !